Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Philippe Cubry,Alain Ghesquière,Kim Nhung Ta,Laurence Albar,Honoré Kam,Anne-Céline Thuillet,Harold Chrestin,Hélène Pidon,Stefan Jouannic,Hélène Adam,François Sabot,Christine Tranchant-Dubreuil,Yves Vigouroux,Olivier François,Maria Holzinger

doi:10.1186/s12284-020-00424-1

Abstract

BackgroundAfrican rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species.ResultsUsing a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations.ConclusionOur results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

Highlights

African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties
The phenotypic data were obtained from infield experiments, Table 1 List of traits and variables used for the association study
We report on the results of an extensive Genome Wide Association Study carried out for several traits of agronomical interest on African rice

Summary

Introduction

Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Its domestication took place in the inner delta of the Niger river (Cubry et al 2018), from a wild relative species, Oryza barthii A. Its origin from this wild Sahelian species explains its strong tolerance or resistance to biotic and abiotic stresses (Sarla and Swamy 2005). In the context of increasing temperatures and a more variable climate, strong tolerance to such stresses is an important objective for rice agriculture worldwide. With the exception of salinity tolerance (Meyer et al 2016), few association studies have been performed for traits of agricultural interest in this species.

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Discussion

Conclusion